1 Samples table

2 Genotyping: raw RNA vs RNA

  • compare SNPs from 40 RNA BAM files to each other
  • percentage values indicate the percentage of SNPs matched based on gtcheck
  • here, unfiltered/raw VCFs were used

3 Genotyping: filtered RNA vs RNA

  • here, use QC-filtered VCFs

4 Genotyping: DNA vs RNA

  • compare SNPs from 40 RNA BAM files to SNPs from donor Neurochip data
  • percentage values indicate the percentage of SNPs matched based on gtcheck

  • same as above, reorder DNA donor samples on x-axis

5 SessionInfo

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.2.0 (2022-04-22)
##  os       macOS Big Sur/Monterey 10.16
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_GB.UTF-8
##  ctype    en_GB.UTF-8
##  tz       Europe/London
##  date     2022-12-09
##  pandoc   2.18 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/tools/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package     * version date (UTC) lib source
##  abind         1.4-5   2016-07-21 [1] CRAN (R 4.2.0)
##  assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.2.0)
##  backports     1.4.1   2021-12-13 [1] CRAN (R 4.2.0)
##  broom         1.0.1   2022-08-29 [1] CRAN (R 4.2.0)
##  bslib         0.4.1   2022-11-02 [1] CRAN (R 4.2.0)
##  cachem        1.0.6   2021-08-19 [1] CRAN (R 4.2.0)
##  callr         3.7.3   2022-11-02 [1] CRAN (R 4.2.0)
##  car           3.1-1   2022-10-19 [1] CRAN (R 4.2.0)
##  carData       3.0-5   2022-01-06 [1] CRAN (R 4.2.0)
##  cli           3.4.1   2022-09-23 [1] CRAN (R 4.2.0)
##  codetools     0.2-18  2020-11-04 [1] CRAN (R 4.2.0)
##  colorspace    2.0-3   2022-02-21 [1] CRAN (R 4.2.0)
##  crayon        1.5.2   2022-09-29 [1] CRAN (R 4.2.0)
##  crosstalk     1.2.0   2021-11-04 [1] CRAN (R 4.2.0)
##  data.table  * 1.14.6  2022-11-16 [1] CRAN (R 4.2.0)
##  DBI           1.1.3   2022-06-18 [1] CRAN (R 4.2.0)
##  devtools      2.4.5   2022-10-11 [1] CRAN (R 4.2.0)
##  digest        0.6.30  2022-10-18 [1] CRAN (R 4.2.0)
##  dplyr         1.0.10  2022-09-01 [1] CRAN (R 4.2.0)
##  DT          * 0.26    2022-10-19 [1] CRAN (R 4.2.0)
##  ellipsis      0.3.2   2021-04-29 [1] CRAN (R 4.2.0)
##  evaluate      0.18    2022-11-07 [1] CRAN (R 4.2.0)
##  fansi         1.0.3   2022-03-24 [1] CRAN (R 4.2.0)
##  farver        2.1.1   2022-07-06 [1] CRAN (R 4.2.0)
##  fastmap       1.1.0   2021-01-25 [1] CRAN (R 4.2.0)
##  fs            1.5.2   2021-12-08 [1] CRAN (R 4.2.0)
##  generics      0.1.3   2022-07-05 [1] CRAN (R 4.2.0)
##  ggplot2     * 3.4.0   2022-11-04 [1] CRAN (R 4.2.0)
##  ggpubr      * 0.5.0   2022-11-16 [1] CRAN (R 4.2.0)
##  ggsignif      0.6.4   2022-10-13 [1] CRAN (R 4.2.0)
##  glue          1.6.2   2022-02-24 [1] CRAN (R 4.2.0)
##  gtable        0.3.1   2022-09-01 [1] CRAN (R 4.2.0)
##  highr         0.9     2021-04-16 [1] CRAN (R 4.2.0)
##  htmltools     0.5.3   2022-07-18 [1] CRAN (R 4.2.0)
##  htmlwidgets   1.5.4   2021-09-08 [1] CRAN (R 4.2.0)
##  httpuv        1.6.6   2022-09-08 [1] CRAN (R 4.2.0)
##  jquerylib     0.1.4   2021-04-26 [1] CRAN (R 4.2.0)
##  jsonlite      1.8.3   2022-10-21 [1] CRAN (R 4.2.0)
##  knitr       * 1.41    2022-11-18 [1] CRAN (R 4.2.0)
##  labeling      0.4.2   2020-10-20 [1] CRAN (R 4.2.0)
##  later         1.3.0   2021-08-18 [1] CRAN (R 4.2.0)
##  lifecycle     1.0.3   2022-10-07 [1] CRAN (R 4.2.0)
##  magrittr      2.0.3   2022-03-30 [1] CRAN (R 4.2.0)
##  memoise       2.0.1   2021-11-26 [1] CRAN (R 4.2.0)
##  mime          0.12    2021-09-28 [1] CRAN (R 4.2.0)
##  miniUI        0.1.1.1 2018-05-18 [1] CRAN (R 4.2.0)
##  munsell       0.5.0   2018-06-12 [1] CRAN (R 4.2.0)
##  pillar        1.8.1   2022-08-19 [1] CRAN (R 4.2.0)
##  pkgbuild      1.4.0   2022-11-27 [1] CRAN (R 4.2.0)
##  pkgconfig     2.0.3   2019-09-22 [1] CRAN (R 4.2.0)
##  pkgload       1.3.2   2022-11-16 [1] CRAN (R 4.2.0)
##  prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.2.0)
##  processx      3.8.0   2022-10-26 [1] CRAN (R 4.2.0)
##  profvis       0.3.7   2020-11-02 [1] CRAN (R 4.2.0)
##  promises      1.2.0.1 2021-02-11 [1] CRAN (R 4.2.0)
##  ps            1.7.2   2022-10-26 [1] CRAN (R 4.2.0)
##  purrr         0.3.5   2022-10-06 [1] CRAN (R 4.2.0)
##  R6            2.5.1   2021-08-19 [1] CRAN (R 4.2.0)
##  Rcpp          1.0.9   2022-07-08 [1] CRAN (R 4.2.0)
##  remotes       2.4.2   2021-11-30 [1] CRAN (R 4.2.0)
##  rlang         1.0.6   2022-09-24 [1] CRAN (R 4.2.0)
##  rmarkdown     2.18    2022-11-09 [1] CRAN (R 4.2.0)
##  rstatix       0.7.1   2022-11-09 [1] CRAN (R 4.2.0)
##  rstudioapi    0.14    2022-08-22 [1] CRAN (R 4.2.0)
##  sass          0.4.4   2022-11-24 [1] CRAN (R 4.2.0)
##  scales        1.2.1   2022-08-20 [1] CRAN (R 4.2.0)
##  sessioninfo   1.2.2   2021-12-06 [1] CRAN (R 4.2.0)
##  shiny         1.7.3   2022-10-25 [1] CRAN (R 4.2.0)
##  stringi       1.7.8   2022-07-11 [1] CRAN (R 4.2.0)
##  stringr       1.5.0   2022-12-02 [1] CRAN (R 4.2.0)
##  tibble        3.1.8   2022-07-22 [1] CRAN (R 4.2.0)
##  tidyr         1.2.1   2022-09-08 [1] CRAN (R 4.2.0)
##  tidyselect    1.2.0   2022-10-10 [1] CRAN (R 4.2.0)
##  urlchecker    1.0.1   2021-11-30 [1] CRAN (R 4.2.0)
##  usethis       2.1.6   2022-05-25 [1] CRAN (R 4.2.0)
##  utf8          1.2.2   2021-07-24 [1] CRAN (R 4.2.0)
##  vctrs         0.5.1   2022-11-16 [1] CRAN (R 4.2.0)
##  withr         2.5.0   2022-03-03 [1] CRAN (R 4.2.0)
##  xfun          0.35    2022-11-16 [1] CRAN (R 4.2.0)
##  xtable        1.8-4   2019-04-21 [1] CRAN (R 4.2.0)
##  yaml          2.3.6   2022-10-18 [1] CRAN (R 4.2.0)
## 
##  [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
## 
## ──────────────────────────────────────────────────────────────────────────────